5.5 3D-Settings

This page describes all options concerning the 3d-mode. Those can be accessed by 'Open 3D Settings' .

Geometric Detail

In this menu you can set up parameters used when a 3D object is created.

NOTE: These settings do not only affect the rendering performance but also play a major role at collision detection. This means that higher settings increase the correctness and minimize overlaps between molecules while a lower setting speeds up the collision detection significantly.

In order to apply any changes for already constructed objects, use the 'Refresh Geometry' button located in the toolbar.

Shape Collision and Construction

First of all you can choose to activate the Shape Collision. Using this option, the molecules will be completely surrounded by shapes. However, if you have a lipid with free space between its tails, this space will be connected. So the overlapping of different lipids is deactivated. If you deactivate this option, the Collision Detection will work faster.

Then you will have to choose between automatic or custom detail settings. Automatic detail ensures that really all the atoms get involved in the construction of the shape. Custom detail does not guarantee that, but it may lead to a better performance, particularly when the molecules get parsed for the first time.

If custom detail is selected, you will be able to access the following 3 sliders:

Precision Modifier

The dependency between the size of a molecule and the number of levels used while constructing its 3d object in vertical order. The value you enter represents the number of Levels x (height/100)

Min. Precision

Ensures that all molecules have at least a minimum detail, e.g. when one is very small

Number of Vertices

The number of vertices that are taken into account for an object. The higher the value, the more vertices per level will be used

The objects at lowest detail settings possible

The objects when higher detail settings are used

Atom Collision

This section allow you to choose whether you want to respect the atom radii during collision detection, too. If you enable this feature you will be able to define an additional minimal distance between the atoms of two molecules. This may be interesting if you prefer uncongested membranes where atoms are not too close to each other, as some molecular dynamic tools do.

NOTE: It is possible to deactivate Shape and Atom Collision. This maybe interesting, if you want to shift different Molecules very close to each other. But using Membrane Algorithms, some of them will not work at all and/or will not terminate. So remember to activate the collision detection again.

Appearance

Brightness Ambient Light

Changes the overall brightness of all visible objects in view.

A high and a low ambient light setting

Directional Lights

Toggles the 2 additional light sources on or off

Left: All light sources on. Right: All light sources off

Shininess Proteins / Lipids

Sets the intensity of light reflection on molecule surfaces. The settings for proteins and lipids are done seperately

A high and a low shininess

Polygon Mode

You can choose between the 2 possible modes for rendering the objects:

With a closed surface (Filled) or

in their transparent triangle mesh (Wireframe)

The filled polygon mode

If you display the objects in the mesh-mode, they become transparent

Visualization

Show all layers is only relevant if multiple monolayers and/or bilayers were added to the membrane model. Normally, only the active membrane layer is visible, the other layers are transparent. If this option is activated, all layers are shown.

Parallel Projection will show the membrane using a parallel perspective. This may make sense for analytic purposes.

The Antialiasing option uses the Java3D antialiasing mode. This mode may not work with every graphic card and usually generates unsatisfactory results. You are recommended to use the antialiasing options of your graphic card driver if available.

Sometimes a Uniform Background is needed. For this purpose it can be activated here. If you want to change the brightness of the background (dark or bright), please use the GUI -> Editor Appearance menu.

Controls Performance

Mouse Sensitivity

Sets the mouse sensitivity for looking around in the 3D view

Dragging of Proteins

Enables or disables the capability to move proteins while using the Free-Look mode. Disabling will avoid annoying unintended displacements

PPE Automatic Protein Placement

If this option is enabled, the MembraneEditor will use available OPM or PDBTM data and automatically align a protein when it gets added.

Fast Transitions

If fast transitions are enabled, you may experience a faster, but less smooth transition, e.g. when deleting groups of molecules, when switching modes etc.

Atom Performance Mode

In this mode, ca. 50 % more atoms can be visualized. If the settings for this mode are changed, please restart the MembraneEditor.

Only for the shape-based visualization, there is no difference in performance. The drawback of this mode is that each atom of the same type has the same atomic structure. Therefore, algorithms like the Atom Level Minimizer will not work correctly, because each time the atom's position of a single lipid of type 1 will be changed, the same atom in each lipid of the same type 1 will change its position (of course, relative to the local origin of each lipid). In addition, the Molecule Editor will be deactivated, because this editor depends on single atom handling. For regular lipid packing algorithms (which do not change the internal, atomic structure of the molecules), this mode will compute the same results.